Egypt's academic life is being stifled by intimidation and censorship imposed by the state, Human Rights Watch says.
Women are "harassed" for not wearing full Islamic dress
The repressive atmosphere has led to self-censorship in the country's universities, the US-based group adds.
It listed a heavy police presence, strict censorship on library books and research topics as some of the main violations of academic freedom.
"Persistent violations of academic freedom have badly undermined Egypt's standing," the group said.
Egypt prides itself on being an educational leader in the Arab world, says the BBC's Heba Saleh in Cairo.
Human Rights Watch says it has discussed its findings with Egyptian officials and was told the government was considering some reforms to the system.
The group spoke to professors, students, state officials, lawyers, journalists, foreign diplomats and representatives of NGOs between 2003 and 2005.
In a 107-page report, the group says academics told its researchers that there are a number of subjects - notably politics, religion and sex - that they do not feel free to discuss publicly.
"State security forces detain and sometimes abuse activists who run for student union offices or demonstrate on campus," the group's deputy Middle East director, Joe Stork, said.
"State-appointed deans interfere with class discussions and the selection of research topics," he added.
The report also criticised a law that requires all imported material, including course books, to be reviewed by the censor's office.
The group said the government of President Hosni Mubarak and the country's Islamist movement are behind some of the worst violations.
"Though Islamist militants are often at odds with government authorities and the target of crackdowns themselves, they have come to exert restrictive influence on university campuses," the report said.
"Islamist students at the national universities often harass liberal female classmates for not wearing... a full veil. Non-Muslims are also victims of this discrimination," it added.
The authorities "should end their excessive and arbitrary interference in the activities of scholars, students and universities", Mr Stork said.